"EF-S" initially stood for "Short-back Focus". One example of this designation comes from the 20 Years of Canon EOS document that states:

"The launch of the EOS 300D also saw the debut of the new EF-S lens mount, the ‘S’ standing for ‘Short-back Focus,’ due to the fact that rear element of the lens is closer to the image sensor than in a regular SLR."

Also, if you look at p. 128 of EF Lens Work III (it's in section 7, The Basics of Interchangeable Lenses...), there's a notation that, "* Some of the EF-S lenses does not employ a short back focus optical system." Yes, that's grammatically incorrect, but correctly quoted, and highlights the fact that while all EF-S lenses have a small image circle, not all of them have a short back focus design (I believe, for example, that the EF-S 17-85mm does not have a short back focus optical design)."